- s -

• s_bv : xg::XG
• s_bv_rank : xg::XG
• s_bv_select : xg::XG
• s_iv : xg::XG
• safe_to_get : vg::VcfBuffer
• sam_files : vg::HTSWriter
• sam_header : vg::HTSWriter
• sample_counter : vg::NGSSimulator
• sample_interval : vg::RebuildParameters
• sample_name : vg::Alignment , vg::MCMCCaller , vg::MinimizerMapper , vg::MultipathAlignment , vg::MultipathAlignmentEmitter , vg::VCFOutputCaller
• sample_names : vg::Deconstructor
• sample_ploidys : vg::Deconstructor
• sample_range : vg::HaplotypeIndexer
• sample_to_haplotypes : vg::Deconstructor::NestingInfo
• sample_to_ploidy : vg::ParentGenotypeInfo
• sample_unsheared_paths : vg::NGSSimulator
• samplers : vg::NGSSimulator::MarkovDistribution< From, To >
• samples : GBWTConfig
• samples_in_batch : vg::HaplotypeIndexer
• save_explanations : vg::Explainer
• scc_copy_count : vg::DagifiedGraph
• scc_of_handle : vg::DagifiedGraph
• score : vg::algorithms::TracedScore , vg::Alignment , vg::AlignmentChainModelVertex , vg::Connection , vg::Funnel::Item , vg::GaplessExtension , vg::Genotyper::Affinity , vg::GFFRecord , vg::MEMChainModelVertex , vg::MEMClusterer::HitNode , vg::MinimizerMapper::Minimizer , vg::Recombinator::Statistics , vg::SnarlDistanceIndexClusterer::Cluster , vg::Subpath , vg::WFAAlignment , vg::WFAPoint
• score_bound : vg::WFATree
• score_matrix : vg::GSSWAligner
• scores : vg::Recombinator::LocalHaplotype
• scratch : vg::ChainIterator
• search_threads : GBWTConfig
• secondary_rescue_attempts : vg::MultipathMapper
• secondary_rescue_score_diff : vg::MultipathMapper
• secondary_rescue_subopt_diff : vg::MultipathMapper
• secondary_score : vg::Alignment
• seed : vg::MCMCGenotyper , vg::NGSSimulator , vg::SnarlDistanceIndexClusterer::SeedCache , vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem , vg::SpliceRegion , vg::StreamSorter< Message > , vg::ZipCodeTree::oriented_seed_t
• seed_count_prefix_sum : vg::SnarlDistanceIndexClusterer::ClusteringProblem
• seed_indices : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild
• seed_length : vg::algorithms::Anchor
• seed_sort_order : vg::ZipCodeForest::forest_growing_state_t
• seeds : vg::BandedGlobalAligner< IntType >::BAMatrix , vg::SnarlDistanceIndexClusterer::Cluster , vg::ZipCodeForest::forest_growing_state_t
• seek : hFILE_backend
• seen_read_names : vg::ReadFilter< Read >
• segment_to_name : vg::FlatFileBackTranslation
• segment_translation : GBWTConfig
• SEPARATOR : handlegraph::PathMetadata
• seq : vg::algorithms::kmer_t , vg::algorithms::walk_t , vg::kmer_t , vg::Region , vg::VG::Plan
• seq_length : vg::Viz , xg::XG
• seq_offset : vg::MatchPos , vg::WFAAlignment , vg::WFAPoint
• sequence : vg::Alignment , vg::Edit , vg::ExtraNodeGraph , vg::KmerMatch , vg::MultipathAlignment , vg::Node , vg::PathIndex , vg::Primer , vg::Recombinator::LocalHaplotype , vg::WFATree
• sequence_id : vg::FragmentedHaplotypeVisit , vg::GFFRecord , vg::RecombinatorFragment , vg::RecombinatorHaplotype
• sequence_source : GraphHandler
• sequence_visits : vg::PrimerPair
• sequences : vg::Haplotypes::Subchain
• set_refpos : vg::MinimizerMapper
• sha1_variant_name : vg::Constructor
• shift_prune_diff : vg::Surjector
• short_mem_filter_factor : vg::BaseMapper
• short_option : vg::subcommand::BaseArgSpec< Receiver >
• short_options : vg::ConfigurableParser
• short_opts : vg::BaseOption< Value, Parser >
• short_read_minimizer_k : vg::IndexingParameters
• short_read_minimizer_w : vg::IndexingParameters
• short_read_minimizer_W : vg::IndexingParameters
• show_cnv : vg::Viz
• show_dna : vg::Viz
• show_path_info : vg::Deconstructor
• show_paths : vg::Viz
• show_progress : GBWTConfig , vg::GBWTHandler , vg::Genotyper , vg::GraphCaller , vg::Progressive , vg::RebuildParameters , vg::Transcriptome , vg::VGset
• show_work : vg::MinimizerMapper
• sibling_indices_at_depth : vg::ZipCodeForest::forest_growing_state_t
• sigma : vg::FragmentLengthDistribution
• simplify_topologies : vg::MultipathMapper
• simultaneous_pair_alignment : vg::Mapper
• since_last_fragment_length_estimate : vg::FragmentLengthStatistics
• sink_fwd : vg::SourceSinkOverlay
• sink_id : vg::SourceSinkOverlay
• sink_nodes : vg::BandedGlobalAligner< IntType >
• sink_rev : vg::SourceSinkOverlay
• site_ends : vg::PhasedGenome
• site_manager : vg::SmallSnarlSimplifier
• site_starts : vg::PhasedGenome
• sites : vg::PhasedGenome::Haplotype
• size : job_type , vg::algorithms::Anchor , vg::str_view
• skip_alt : vg::VCFTraversalFinder
• skip_structural_duplications : vg::VariantAdder
• skippable : vg::algorithms::Anchor
• snarl : vg::ReplaceSnarlHaplotypeCommand , vg::SnarlManager::SnarlRecord , vg::Visit
• snarl_caller : vg::GraphCaller
• SNARL_CHAIN_COMPONENT_OFFSET : vg::ZipCode
• SNARL_CHILD_COUNT_OFFSET : vg::ZipCode
• snarl_into : vg::SnarlManager
• SNARL_IS_REGULAR_OFFSET : vg::ZipCode
• SNARL_LENGTH_OFFSET : vg::ZipCode
• snarl_manager : vg::ExhaustiveTraversalFinder , vg::FlowTraversalFinder , vg::GraphCaller , vg::Masker , vg::MCMCCaller , vg::MultipathMapper , vg::NestedTraversalFinder , vg::PathRestrictedTraversalFinder , vg::PhasedGenome , vg::ReadRestrictedTraversalFinder , vg::RegionExpander , vg::RepresentativeTraversalFinder , vg::SnarlGraph , vg::SupportBasedSnarlCaller , vg::TraversalSupportFinder , vg::VCFTraversalFinder
• snarl_number : vg::SnarlManager::SnarlRecord
• SNARL_OFFSET_IN_CHAIN_OFFSET : vg::ZipCode
• snarl_rank_or_identifier : vg::ZipCode::chain_code_t
• snarl_reference_length_histogram : vg::Genotyper
• snarl_traversals : vg::Genotyper
• snarlmanager : vg::PathBasedTraversalFinder
• snarls : vg::MCMCGenotyper , vg::SnarlGraph , vg::SnarlManager
• soft_clip_limit : vg::Filter
• soft_clipped : vg::Alignment
• softclip_threshold : vg::Mapper
• sort_by_chain_score : vg::MinimizerMapper
• sort_value : vg::ZipCodeForest::sort_value_t
• sort_values_by_seed : vg::ZipCodeForest::forest_growing_state_t
• source : vg::algorithms::TracedScore , vg::GFFRecord , vg::SnarlDistanceIndexClusterer::Seed
• source_fwd : vg::SourceSinkOverlay
• source_id : vg::SourceSinkOverlay
• source_nodes : vg::BandedGlobalAligner< IntType >
• source_paths : vg::NGSSimulator , vg::Sampler
• source_rev : vg::SourceSinkOverlay
• space_efficient_counting : vg::IndexingParameters
• sparse_to_dense : vg::SparseUnionFind
• splice_rescue_graph_std_devs : vg::MultipathMapper
• splice_stats : vg::MultipathMapper
• SPLICED_DEFAULT_SUBGRAPH_LIMIT : vg::Surjector
• split_read_limit : vg::Filter
• split_supports : vg::BREAKPOINT
• stable : vg::GAFSorterParameters
• stack_data : vg::ZipCodeTree::reverse_iterator
• stage_name : vg::Funnel
• stage_start_time : vg::Funnel
• stages : vg::Funnel
• STANDARD_LIBRARY : vg::Version
• star_allele : vg::Deconstructor
• start : gafkluge::GafStep , MappingRun , ReferenceInterval , vg::algorithms::Anchor , vg::BREAKPOINT , vg::GFFRecord , vg::GraphSynchronizer::Lock , vg::HaplotypePartitioner::Subchain , vg::Haplotypes::Subchain , vg::MultipathAlignment , vg::NetGraph , vg::Range< Number > , vg::Region , vg::Snarl
• start_end_reachable : vg::Snarl
• start_offset : vg::algorithms::Anchor
• start_pos : vg::algorithms::Anchor , vg::MEMClusterer::HitNode
• start_pos_samplers : vg::NGSSimulator
• start_seed : vg::algorithms::Anchor
• start_self_reachable : vg::Snarl
• start_time : vg::Funnel
• start_zip : vg::algorithms::Anchor
• state : haplo::haplo_DP_rectangle , vg::GaplessExtension , vg::GenomeState , vg::Watchdog , vg::WFANode
• states : vg::PhaseUnfolder
• stdev : vg::SummaryStatistics
• step : handlegraph::PathForEachSocket::iterator , vg::Range< Number >
• steps : vg::IndexingPlan
• steps_of_handle_memo : vg::MemoizingGraph
• stop_on_duplicate_paths : vg::algorithms::GFAParser
• stop_time : vg::Funnel
• stop_watcher : vg::Watchdog
• strand : gafkluge::GafRecord
• strand_is_rev : vg::GFFRecord
• strand_sampler : vg::NGSSimulator
• strict_conflict_checking : vg::Deconstructor
• strip_bonuses : vg::BaseMapper
• stripped_match_alg_max_length : vg::MultipathMapper
• stripped_match_alg_strip_length : vg::MultipathMapper
• stripped_match_alg_target_count : vg::MultipathMapper
• sub_durations : vg::Funnel::Stage
• sub_mem_count_thinning : vg::BaseMapper
• sub_mem_thinning_burn_in : vg::BaseMapper
• sub_poly_rate : vg::NGSSimulator
• sub_score : vg::ReadFilter< Read >
• subchain_id : vg::RecombinatorFragment
• subchain_length : vg::HaplotypePartitioner::Parameters
• SUBCHAIN_LENGTH : vg::HaplotypePartitioner
• subchains : vg::Haplotypes::TopLevelChain , vg::Recombinator::Statistics
• subgraph : vg::GraphSynchronizer::Lock , vg::SpliceRegion
• subgraph_min : PruningParameters
• subgraph_prune : vg::VariantAdder
• subgroups : vg::subcommand::GroupedOptionGroup
• subpath : vg::MultipathAlignment
• subpath_handles : vg::SubpathOverlay
• subpath_to_length : vg::HTSWriter
• subsequences : vg::ReadFilter< Read >
• substage_name : vg::Funnel
• substage_start_time : vg::Funnel
• suffix : vg::IndexFile
• suffixes : vg::PhaseUnfolder
• suggested_edges : vg::DiagramExplainer
• sum : haplo::haplo_DP_column
• super : handlegraph::algorithms::SubHandleGraph , vg::PathSubgraph , vg::SubHandleGraph , vg::TreeSubgraph
• support : vg::LocationSupport , vg::Locus
• support_finder : vg::SupportBasedSnarlCaller
• suppress_cluster_merging : vg::MultipathMapper
• suppress_mismapping_detection : vg::MultipathMapper
• suppress_multicomponent_splitting : vg::MultipathMapper
• suppress_p_value_memoization : vg::MultipathMapper
• suppress_tail_anchors : vg::MultipathMapper
• surface : vg::Viz
• surject_subpath_global : vg::SurjectingAlignmentEmitter
• surjector : vg::SurjectingAlignmentEmitter
• SV_TYPE : vg::BREAKPOINT
• symbol_count : vg::Pictographs
• symbolic_allele_warnings : vg::Constructor
• symbols : vg::Pictographs
• sync : vg::VariantAdder
• synchronizer : vg::GraphSynchronizer::Lock